Accelerating genomic sequence alignment using high performance reconfigurable computers

Simple item page
dc.contributor.advisorKuttel, Michelle Maryen_ZA
dc.contributor.authorMcMahon, Peter Leonarden_ZA
dc.date.accessioned2016-02-29T12:07:18Z
dc.date.available2016-02-29T12:07:18Z
dc.date.issued2008en_ZA
dc.descriptionIncludes bibliographical references (pages 65-70).en_ZA
dc.description.abstractReconfigurable computing technology has progressed to a stage where it is now possible to achieve orders of magnitude performance and power efficiency gains over conventional computer architectures for a subset of high performance computing applications. In this thesis, we investigate the potential of reconfigurable computers to accelerate genomic sequence alignment specifically for genome sequencing applications. We present a highly optimized implementation of a parallel sequence alignment algorithm for the Berkeley Emulation Engine (BEE2) reconfigurable computer, allowing a single BEE2 to align simultaneously hundreds of sequences. For each reconfigurable processor (FPGA), we demonstrate a 61X speedup versus a state-of-the-art implementation on a modern conventional CPU core, and a 56X improvement in performance-per-Watt. We also show that our implementation is highly scalable and we provide performance results from a cluster implementation using 32 FPGAs. We conclude that reconfigurable computers provide an excellent platform on which to run sequence alignment, and that clusters of reconfigurable computers will be able to cope far more easily with the vast quantities of data produced by new ultra-high-throughput sequencers.en_ZA
dc.identifier.apacitationMcMahon, P. L. (2008). <i>Accelerating genomic sequence alignment using high performance reconfigurable computers</i>. (Thesis). University of Cape Town ,Faculty of Science ,Department of Computer Science. Retrieved from http://hdl.handle.net/11427/17377en_ZA
dc.identifier.chicagocitationMcMahon, Peter Leonard. <i>"Accelerating genomic sequence alignment using high performance reconfigurable computers."</i> Thesis., University of Cape Town ,Faculty of Science ,Department of Computer Science, 2008. http://hdl.handle.net/11427/17377en_ZA
dc.identifier.citationMcMahon, P. 2008. Accelerating genomic sequence alignment using high performance reconfigurable computers. University of Cape Town.en_ZA
dc.identifier.ris TY - Thesis / Dissertation AU - McMahon, Peter Leonard AB - Reconfigurable computing technology has progressed to a stage where it is now possible to achieve orders of magnitude performance and power efficiency gains over conventional computer architectures for a subset of high performance computing applications. In this thesis, we investigate the potential of reconfigurable computers to accelerate genomic sequence alignment specifically for genome sequencing applications. We present a highly optimized implementation of a parallel sequence alignment algorithm for the Berkeley Emulation Engine (BEE2) reconfigurable computer, allowing a single BEE2 to align simultaneously hundreds of sequences. For each reconfigurable processor (FPGA), we demonstrate a 61X speedup versus a state-of-the-art implementation on a modern conventional CPU core, and a 56X improvement in performance-per-Watt. We also show that our implementation is highly scalable and we provide performance results from a cluster implementation using 32 FPGAs. We conclude that reconfigurable computers provide an excellent platform on which to run sequence alignment, and that clusters of reconfigurable computers will be able to cope far more easily with the vast quantities of data produced by new ultra-high-throughput sequencers. DA - 2008 DB - OpenUCT DP - University of Cape Town LK - https://open.uct.ac.za PB - University of Cape Town PY - 2008 T1 - Accelerating genomic sequence alignment using high performance reconfigurable computers TI - Accelerating genomic sequence alignment using high performance reconfigurable computers UR - http://hdl.handle.net/11427/17377 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/17377
dc.identifier.vancouvercitationMcMahon PL. Accelerating genomic sequence alignment using high performance reconfigurable computers. [Thesis]. University of Cape Town ,Faculty of Science ,Department of Computer Science, 2008 [cited yyyy month dd]. Available from: http://hdl.handle.net/11427/17377en_ZA
dc.language.isoengen_ZA
dc.publisher.departmentDepartment of Computer Scienceen_ZA
dc.publisher.facultyFaculty of Scienceen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.subject.otherComputer Scienceen_ZA
dc.titleAccelerating genomic sequence alignment using high performance reconfigurable computersen_ZA
dc.typeMaster Thesis
dc.type.qualificationlevelMasters
dc.type.qualificationnameMScen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceThesisen_ZA
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
thesis_sci_2008_mcmahon_peter_leonard.pdf
Size:
987.37 KB
Format:
Adobe Portable Document Format
Description:
Download
Collections
Masters